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Analysis of the Root Nodule-enhanced Transcriptome in Soybean
안정선,Cheol-Goo Hur,오창재,김호방,Sun-Yong Park 한국분자세포생물학회 2004 Molecules and cells Vol.18 No.1
For high throughput screening of root nodule-enhanced genes, cDNA libraries specific for three different developmental stages of soybean root nodules were constructed after inoculation with Bradyrhizobium japonicum USDA110. 5,469 cDNA clones were sequenced and grouped into 2,511 non-redundant (nr) ESTs consisting of 769 contigs and 1,742 singletons. Using similarity searches against several public databases we constructed a functional classification of the ESTs into root nodule-specific nodulin genes, stress-responsive genes and genes related to carbon and nitrogen metabolism. We also constructed a cDNA microarray with 382 selected clones that appeared to be up-regulated in the root nodule. Using the microarray we compared the transcript levels of uninfected roots and root nodules from four developmental stages. We identified 81 genes that were differentially expressed, and grouped them into seven clusters according to the similarity of their expression profiles, using a hierarchical clustering algorithm. Clusters 1, 2, 3, and 6, comprised of 58 genes, showed root nodule-enhanced expression. The information from this study will be used to analyze the roles of root nodule-specific genes and signaling pathways during root nodule development.
Inhibitory Effect of Gamisaenghyeolyunbueum on Mast Cell-Mediated Allergic Inflammatory Reactions
Choi Cheol-Ho,Hur Jong-Chan,Kim Hoon,Cho Young-Kee,Moon Mi-Hyun,Baek Dong-Gi,Kim Dong-Woung,Moon Goo,Won Jin-Hee The Physiological Society of Korean Medicine 2005 동의생리병리학회지 Vol.19 No.5
Gamisaenghyeolyunbueum (GSYE) is a traditional Oriental herbal medicine prescription, which has been used for the treatment of various allergic disorders, atopic dermatitis, extravasated bleeding from skin, especially skin related disease. The author investigated the effects of GSYE on mast cell-mediated allergic inflammatory reactions. GSYE dose-dependently (0.01-1 g/kg) inhibited compound 48180-induced systemic anaphylactic shock and ear swelling response. The inhibitory effect of GSYE on the histamine release from rat peritoneal mast cells induced by compound 48f80 reveals significantly (p<0.05) at concentrations ranging from 0.01 to 1 mg/ml in a dose-dependent manner. GSYE also inhibited the passive cutaneous anaphylaxis(PCA) by oral administration at 1 g/kg. In addition, GSYE dose-dependently (0.01-1 g/kg) inhibited the phorbol 12-myristate 13-acetate(PMA) and A23187-induced tumor necrosis $factor-{\alpha}$ secretion from human mast cell line HMC-1 cells. These results indicate that GSYE may be a beneficial applicability in the allergic-related diseases.
A computational approach for identifying pathogenicity islands in prokaryotic genomes
Yoon, Sung Ho,Hur, Cheol-Goo,Kang, Ho-Young,Kim, Yeoun Hee,Oh, Tae Kwang,Kim, Jihyun F BioMed Central 2005 BMC bioinformatics Vol.6 No.-
<P><B>Background</B></P><P>Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs.</P><P><B>Results</B></P><P>We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs.</P><P><B>Conclusion</B></P><P>Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis.</P>